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• A model predictive control-based energy management for an electro-thermal microgrid. • The strategy minimizes operating costs and pollution avoiding battery degradation. • Analyze the state of health of the battery system to reduce degradation. • A comparison with a Unit Commitment approach under different generation scenarios. Access to electricity is a fundamental key to developing countries' growth. Microgrids (MG) have become potential solutions to provide energy to isolated rural areas in a safe and environmentally friendly way. Therefore, proposals for alternative solutions to bridge the electrification gap in the Ecuadorian Amazon – which has the most significant percentage of its population without access to electricity – are of significant interest. Consequently, this paper presents the design of an Energy Management System (EMS) based on Model Predictive Control (MPC) for an isolated electro-thermal microgrid comprising a photovoltaic generator, a diesel generator, a lithium-ion battery Energy Storage System (ESS), electrical loads, and a domestic hot water system. The EMS aims to supply energy reliably and safely, minimize the MG's operation costs, and extend the ESS's useful life while satisfying the end users' comfort. This study includes an estimated degradation model for the ESS's State of Health (SOH), an essential parameter contributing to reducing the microgrid's operating costs in the long term. Simulation results using one-year data present the influence of the prediction horizon on the MG's scheduling. In addition, the benefits of the proposed EMS are highlighted by comparing it with the results achieved by a Unit Commitment approach, where it is demonstrated that the proposed EMS presents a reduction in MG operating costs and greenhouse gas emissions while maximizing the utilization of renewable energy and extending the lifespan of the ESS. Finally, an experimental validation, using a Typhoon Hardware-in-the-loop HIL-402 device in real-time operation, stands out the effectiveness and feasibility of the proposed MPC-based EMS. [ABSTRACT FROM AUTHOR]